Mass spectrometers are used to analyze sample substances containing elements or compounds or mixtures of elements or compounds by measuring the mass to charge of ions produced from a sample substance in an ion source. A number of types of ion sources that can produce ions from solid, liquid or gaseous sample substrates have been combined with mass spectrometers. Ions can be produced in vacuum using ion sources, including, but not limited to, Electron Ionization (EI), Chemical Ionization (CI), Laser Desorption (LD), Matrix Assisted Laser Desorption (MALDI), Fast Atom Bombardment (FAB), Field Desorption (FD) or Secondary Ion Mass Spectrometry (SIMS). Alternatively, ions can be produced at or near atmospheric pressure using ion sources, including, but not limited to, Electrospray (ES), Atmospheric Pressure Chemical Ionization (APCI) or Inductively Coupled Plasma (ICP). Ion sources that operate at intermediate vacuum pressures such as Glow Discharge Ion Sources have also been used to generate ions for mass spectrometric analysis. Ion sources that operate in vacuum are generally located in the vacuum region of the mass spectrometer near the entrance to the mass analyzer to improve the efficiency of ion transfer to the detector. Ion sources that produce ions in vacuum have also been located outside the region near the mass spectrometer entrance. The ions produced in a location removed from the mass analyzer entrance must be delivered to the entrance region of the mass spectrometer prior to mass analysis. Atmospheric or intermediate pressure ion sources are configured to deliver ions produced at higher pressure into the vacuum region of the mass analyzer. The geometry and performance of the ion optics used to transport ions from an ion source into the entrance region of a given mass analyzer type can greatly affect the mass analyzer performance. This is particularly the case with Time-Of-Flight mass analyzers, in which the initial spatial and energy distribution of the ions pulsed into the flight tube of a Time-Of-Flight mass analyzer affects the resulting mass to charge analysis resolving power and mass accuracy.
Mass analysis conducted in a Time-Of-Flight mass (TOF) mass spectrometer is achieved by accelerating or pulsing a group of ions into a flight tube under vacuum conditions. During the flight time, ions of different mass to charge values spatially separate prior to impacting a detector surface. Ions are accelerated from a first acceleration or pulsing region and may be subject to one or more acceleration and deceleration regions during the ion flight time prior to impinging on a detector surface. Multiple ion accelerating and decelerating stages configured in Time-Of-Flight mass spectrometers aid in compensating or correcting for the initial ion spatial and energy dispersion of the initial ion population in the first ion pulsing or accelerating region. The most common lens geometry used in the first TOF ion pulsing or accelerating region is two parallel planar electrodes with the electrode surfaces oriented perpendicular to the direction of ion acceleration into the Time-Of-Flight tube. The direction of the initial ion acceleration is generally in a direction parallel with the TOF tube axis. A linear uniform electric field is formed in the gap between the two parallel planar electrodes when different electrical potentials are applied to the two electrodes. The planar electrode positioned in the direction of ion acceleration into the TOF tube is generally configured as a highly transparent grid to allow ions to pass through with minimal interference to the ion trajectories. To maximize the performance of a Time-Of-Flight mass analyzer, it is desirable to initiate the acceleration of ions in the pulsing region with all ions initially positioned in a plane parallel with the planar electrodes and initially having the same initial kinetic energy component in the direction of acceleration. Consequently, when ions are generated in or transported into the initial accelerating or pulsing region of a Time-Of-Flight mass analyzer, conditions are avoided which lead to ion energy or spatial dispersion at the initiation of ion acceleration into the Time-Of-Flight tube drift region. As a practical matter, a population of gaseous phase ions located in the pulsing region will have a non-zero spatial and kinetic distribution prior to pulsing into a Time-Of-Flight tube drift region. This non zero spatial and kinetic energy spread may degrade Time-Of-Flight mass to charge analysis resolving power, sensitivity and mass measurement accuracy. In one aspect of the present invention, the spatial and energy spread of an ion population is minimized prior to accelerating the population of ions into a Time-Of-Flight tube drift region.
When ion spatial and energy spread can not be avoided in the TOF pulsing or first accelerating region, it is desirable to have the ion energy and spatial distributions correlated so that both can be compensated and corrected for during the ion flight time prior to hitting the detector. A correlation between the ion kinetic energy component in the TOF axial direction and spatial spread can occur in the TOF pulsing region when spatially dispersed ions with a non random TOF axial kinetic energy component are accelerated in a uniform electric field formed between two parallel electrodes. Wiley et. al., The Review of Scientific Instruments 26(12):1150-1157 (1955) described the configuration and operation of a second ion accelerating region to refocus ions of like mass to charge along the TOF flight path that start their acceleration with a correlated spatial and energy spread. Electrode geometries in the TOF tube and voltages applied to these electrodes can be varied with this technique to position the focal plane of a packet of ions of the same mass to charge value at the detector surface to achieve maximum resolving power. The Wiley-McClaren focusing technique improves resolving power when ions occupying a finite volume between two parallel plate electrodes are accelerated. In a uniform electric accelerating field, ions of the same m/z value located closer to the repelling electrode will begin their acceleration at a higher potential than an ion of the same m/z initiating its acceleration at a position further from the repelling electrode. The ion that starts its acceleration nearer to the repelling electrode surface at a higher potential, must travel further than the slower ion which starts its acceleration at a lower potential closer to the extraction grid or electrode. At some point in the subsequent ion flight, the faster ion will pass the slower ion of the same m/z value. By adding a second accelerating region, the location of the point where the ions having the same mass to charge value pass and hence are “focused” in a plane, can be optimized to accommodate a desired flight time and flight tube geometry. The focal point occurring in the first field free region in the TOF drift tube can be “reflected” into a second field free region using an ion mirror or reflector in the ion flight path.
Variations in ion flight time can also be caused by initial ion velocity components not correlated to the spatial spread. This non-correlated ion kinetic energy distribution can be compensated for, to some degree, by the addition of an ion reflector or mirror in the ion flight path. Ions of the same m/z value with higher kinetic energy in the TOF axial direction will penetrate deeper into the decelerating field of an ion reflector prior to being re-accelerated in the direction of the detector. The ion with higher kinetic energy experiences a longer flight path when compared to a lower energy ion of the same m/z value. Subjecting an ion to multiple accelerating and decelerating electric fields allows operation of a TOF mass analyzer with higher order focusing to improve resolving power and mass measurement accuracy. Configuration and operation of an Atmospheric Pressure Ion Source Time-Of-Flight mass analyzer with higher order focusing is described by Dresch in U.S. Pat. No. 5,869,829. Higher order focusing corrections can not entirely compensate for initial ion kinetic energy spread in the TOF axial direction that is not correlated with ion spatial spread in the initial pulsing or ion acceleration region. Also, higher order focusing can not entirely compensate for ion energy or spatial spreads which occur during ion acceleration, deceleration or field free flight due to ion fragmentation or ion collisions with neutral background molecules. An ion kinetic energy distribution not correlated to the ion spatial distribution can occur when ionization techniques such as MALDI are used. In MALDI ionization, the sample-bearing surface is located in the initial acceleration region of a Time-Of-Flight mass spectrometer. A laser pulse impinging on a sample surface, in a MALDI ion source, creates a burst of neutral molecules as well as ions in the initial accelerating region of a Time-Of-Flight mass analyzer. Ion to neutral molecule collisions can occur during ion extraction and acceleration into the TOF drift tube resulting in an ion kinetic energy spread, ion fragmentation, degradation of resolving power and errors in mass to charge measurement. This problem increases if structural information via ion fragmentation is desired using MALDI Time-Of-Flight mass analysis. Higher energy laser pulses used in MALDI to increase the ion fragmentation also result in increased neutral molecule ablation from the target surface. Even in the absence of ion-neutral collisions, ions generated from the target surface have an initial velocity or kinetic energy distribution that is not well correlated to spatial distribution in the first ion acceleration region. This initial non-correlated kinetic distribution of the MALDI generated ion population can degrade resolving power, and mass accuracy performance in Time-Of-Flight mass analysis.
A technique, termed delayed extraction, has been developed where the application of an electric field to accelerate ions into the TOF drift tube is delayed after the MALDI laser pulse is applied to allow time for the neutral gas to expand, increasing the mean free path prior to ion acceleration. By applying a small reverse accelerating field during the MALDI laser pulse and delaying the acceleration of ions into the Time-Of-Flight tube drift region, as described by Vestal et. al. in U.S. Pat. No. 5,625,184, some portion of the low m/z ions can be eliminated. A portion of the low m/z ions, primarily matrix related ions, created in the MALDI process are accelerated back to the sample surface and neutralized when the reverse electric field is applied. A portion of the slower moving higher mass to charge ions do not return to the target surface as rapidly as the lower molecular weight ions when the reverse accelerating field is applied. After an appropriate delay, these higher molecular weight ions may be forward accelerated into the TOF tube drift region by switching the electric field applied between the two electrodes in the first ion acceleration region. Delayed extraction also allows many of the ion fast fragmentation processes to occur prior to accelerating ions into the Time-Of-Flight tube drift region, resulting in improved mass to charge resolving power and mass accuracy measurements for the ions produced in fast fragmentation processes. The delayed extraction technique reduces the ion energy deficit which can occur due to ion-neutral collisions in the first accelerating region but does not entirely eliminate it, particularly with higher energy laser pulses. Also, delayed extraction is effective in improving MALDI Time-Of-Flight performance when lasers with longer pulse durations are used. However, even with delayed extraction, there is a limit to the length of delay time, the magnitude of the reverse field during the delay period, the laser power used and the duration of a laser pulse before overall sensitivity or Time-Of-Flight performance is degraded. The delayed extraction technique requires a balancing of several variables to achieve optimal performance, often with compromises to the Time-Of-Flight mass analysis performance over all or some portion of the mass to charge spectrum generated. The present invention improves the performance of MALDI Time-Of-Flight without imposing the restrictions or limitations of conventional delayed extraction techniques and provides more uniform Time-Of-Flight mass analysis performance over a wider mass to charge range.
When ions are generated in an ion source positioned external to the Time-Of-Flight pulsing or first acceleration region, a technique termed “orthogonal” pulsing has been used to minimize effects of the kinetic energy distribution of the initial ion beam. This orthogonal pulsing technique first reported by The Bendix Corporation Research Laboratories Division, Technical Documentary Report No. ASD-TDR-62-644, Part 1, April 1964, has become a preferred technique to interface external ion sources, particularly Atmospheric Pressure Ionization Sources, with Time-Of-Flight mass analyzers. The ion beam produced from an Atmospheric Pressure Ion Source (API) or an ion source that operates in vacuum, is directed into the gap between the two parallel planar electrodes defining the first accelerating region of the TOF mass analyzer. The primary ion beam trajectory is directed to traverse the gap between the two parallel planar electrodes in the TOF first accelerating region substantially orthogonal to axis to the axis of the direction of ion acceleration into Time-Of-Flight tube. When orthogonal pulsing is used, ion kinetic energy in the primary ion beam direction is not coupled to the ion velocity component oriented in the direction of ion acceleration into the Time-Of-Flight tube drift region. The primary ion beam kinetic energy spread oriented along the beam axis only affects the location of ion impact on the planar detector surface, not the ion arrival time at the detector surface. Apparatus and methods have been developed to improve the duty cycle of TOF mass analyzers configured with linear or orthogonal pulsing geometries.
Grix, et. al., in Int. J. Mass Spectrom. Ion Processes 93, 323 (1989) describe an approach for creating and storing ions in the TOF pulsing region between extraction pulses. Sample gas is introduced directly into the TOF pulsing region, and an electron beam is directed to pass through the TOF pulsing region, which ionizes sample gas molecules. The electron beam is sufficiently intense so that the local potential well produced by the electrons traps a substantial number of ions until they are pulsed into the TOF drift region for mass analysis. Several disadvantages of this approach include: 1) sample gas is introduced directly into the TOF optics, degrading the vacuum and causing ion scattering; 2) electron impact ionization results in substantial fragmentation which renders this ionization method impractical for mass analysis of many types of samples, such as large biomolecules; and 3) the sample needs to be introduced into the TOF as a gas, which makes this approach incompatible with non-volatile samples.
Chien, et. al., in Anal. Chem. 66, 1630 (1994), and references therein, describe a configuration which incorporates a Paul three-dimensional RF-quadrupole ion trap as the TOF pulsing region for the TOF mass analysis of ions generated externally by MALDI and by electrospray ionization. Ions can be accumulated in such a trap prior to pulsing the ions out of the trap and into the TOF drift region. However, the continuous transfer of externally-generated ions into such a three-dimensional RF-quadrupole ion trap is problematic because ions with energies great enough to overcome the RF-fields in the trap and enter the trap will generally have too much energy to be trapped once they are in the trap volume. Therefore, complicated schemes are employed with limited success to overcome this difficulty, such as pulsing or ramping the RF voltages on and off in concert with pulsed ion introduction; synchronizing pulsed ion introduction with the phase of the RF waveform; and/or introducing inert gas with which the ions can collide and dissipate kinetic energy during ion trapping. Another disadvantage of this configuration is that the electrode geometry that creates the trapping fields is unable to create the linear fields during the pulsed TOF acceleration necessary for achieving maximum TOF mass resolving power.
Ji, et. al., J. Amer. Soc. Mass Spec. 7, 1009 (1996) describe a three-dimensional planar electrode ion trap configured as the pulsing region of a TOF mass spectrometer. Their approach was to ionize and collect ions directly in the trap by electron-impact ionization of gaseous sample molecules introduced into the trap, and then to pulse the trapped ions into the TOF drift region for mass analysis. This ion optics arrangement is able to produce improved TOF acceleration fields relative to those produced by typical three-dimensional ion traps with curved electrode surfaces. However, a three-dimensional planar-electrode ion trap employed as the pulsing region of a TOF mass spectrometer suffers from difficulties in efficient trapping of ions due to the non-ideal trapping fields, as well as from scattering of ions by the sample gas and by the gas introduced to collisionally cool the ions in the trap, which degrades TOF mass resolution and sensitivity.
Dresch et. al. in U.S. Pat. No. 5,689,111 describe an apparatus and method for improving the duty cycle and consequently the sensitivity of a Time-Of-Flight mass analyzer. Ions contained in a continuous ion beam delivered from an atmospheric pressure ion source into a two-dimensional multipole ion guide, are trapped in the multipole ion guide and selectively released from the ion guide exit into the TOF pulsing region. This apparatus and technique delivers ion packets into the pulsing or first acceleration region of a TOF mass analyzer from a continuous ion beam with higher efficiency and less ion loss than can be achieved with a continuous primary ion beam delivered directly into the TOF pulsing region. Ion trapping of a continuous ion beam in an ion guide effectively integrates ions delivered in the primary ion beam between TOF pulses. When this apparatus and technique is applied to an orthogonal pulsing TOF geometry, portions of the mass to charge range can be prevented from being accelerated into the Time-Of-Flight drift region, reducing unnecessary detector channel dead time, resulting in improved sensitivity and dynamic range. Operation with the orthogonal pulsing technique has provided significant Time-Of-Flight mass analysis performance improvements when compared with the performance using in-line ion beam pulsing techniques.
Franzen in U.S. Pat. No. 5,763,878 describes a multipole ion guide that extends orthogonally into the pulsing region of a TOF mass spectrometer. Ions can be transported from an external ion source into the TOF pulsing region located within a portion of the length of the ion guide, and accelerated orthogonally into the TOF drift region by applying pulsed acceleration voltages to the multipole rods so as to accelerate the ions through the space between two of the rods. One disadvantage of this scheme is that linear acceleration fields required for optimum TOF mass resolving power could not be formed by the inhomogeneous acceleration fields produced by such a multipole rod structure.
Even with orthogonal injection of ions into a pulsed acceleration region with perfectly planar fields, it is not always possible to achieve optimal primary ion beam characteristics in the pulsing region whereby all orthogonal velocity components are eliminated or spatially correlated. An approach intended to overcome such limitations has been described by Whitehouse, et. al., in U.S. Pat. No. 6,040,575. One embodiment of heir invention combines orthogonal ion beam introduction into the TOF pulsing region with ion collection on a surface prior to pulsing the surface collected ion population into the TOF tube drift region. The spatial and energy compression of the ion population on the collecting surface prior to pulsing into the TOF tube drift region improves the Time-Of-Flight mass resolving power and mass accuracy. Their invention also results in improved sensitivity by collecting and storing ions between TOF acceleration pulses that would have been otherwise lost. Further, surface induced dissociation (SID) and subsequent collection, storage, and TOF mass analysis of the resulting fragment ion population is facilitated by directing ions to impact the collecting surface with high energy. However, their approach is practical only if the interaction between the ions and the surface is weak enough so that: 1) the charge on the ions is maintained; 2) the ‘sticking probability’ for the ions on the surface is high enough to capture and hold ions, but low enough to allow the ions to be desorbed intact and without impedance upon application of the acceleration pulse of the time of flight analyzer, possibly with the assistance of some auxiliary desorption process, such as the application of heat, an ion beam pulse, or a laser pulse; and 3) the deposition and desorption processes can be cycled repetitively many times without substantial degradation of the surface characteristics.
One embodiment of the present invention involves ion collection of externally generated ions in an ion trap in the pulsed acceleration region, but rather than collecting ions on a surface, or in the three-dimensional pseudo potential energy well of a typical three-dimensional RF-ion trap, ions are collected instead in a pseudo-potential energy well that is primarily one-dimensional, with the pseudo potential well axis oriented parallel to the flight tube axis, prior to pulsing the collected ion population into the TOF tube drift region. The resulting constraints on the spatial and energy distributions of the ion population prior to pulsing into the TOF drift region improves Time-Of-Flight performance and analytical capability. Further, by allowing the ions to gently collide with the surface or with an inert gas, the spatial and energy distributions of the ion population collected in the one-dimensional pseudo-potential energy well can be compressed, resulting in addition improvement in Time-Of-Flight performance and analytical capability.
The orthogonal pulsing technique has been configured in hybrid or tandem mass spectrometers that include Time-Of-Flight mass analysis. Two or more individual mass analyzers are combined in tandem or hybrid TOF mass analyzers to achieve single or multiple mass to charge selection and fragmentation steps followed by mass analysis of the product ions. Identification and/or structural determination of compounds is enhanced by the ability to perform MS/MS or multiple MS/MS steps (MS/MSn) in a given chemical analysis. It is desirable to control the ion fragmentation process so that the required degree of fragmentation for a selected ion species can be achieved in a reproducible manner. Time-Of-flight mass analyzers have been configured with magnetic sector, quadrupole, ion trap and additional Time-Of-Flight mass analyzers to perform mass selection and fragmentation prior to a final Time-Of-Flight mass analysis step. Gas phase Collisional Induced Dissociation (CID) and Surface Induced Dissociation (SID) techniques have been used to selectively fragment gas phase ions prior to TOF mass analysis or have been coupled to the ion flight path in the Time-Of-Flight tube. CID ion fragmentation has been the most widely used of the two techniques. Magnetic sector mass analyzers have been configured to perform mass to charge selection with higher energy CID fragmentation of mass to charge selected ions to aid in determining the structure of compounds. Lower energy CID fragmentation achievable in quadrupoles, ion traps and Fourier Transform mass analyzers, although useful in many analytical applications, may not provide sufficient energy to effectively fragment all ions of interest. High energy CID fragmentation can yield side chain cleavage fragment ion types such as w type fragments. This type of fragmentation is less common in low energy CID processes. The additional ion fragmentation information achievable with higher energy fragmentation techniques can be useful when determining the structure of a molecule.
An alternative to CID ion fragmentation is the use of Surface Induced Dissociation to fragment ions of interest. The capability of the Surface Induced Dissociation ion fragmentation technique has been reported for a number of mass analysis applications. Wysocki et. al. J. Am. Soc. for Mass Spec., 1992, 3, 27-32 and McCormack et. al., Anal. Chem. 1993, 65, 2859-2872, have demonstrated the use of SID ion fragmentation with quadrupole mass analysis to controllably and reproducibly achieve analytically useful fragmentation information. McCormack et. al. showed that with collisional energies below 100 eV, w and d type ion fragments can be produced from some peptides. Kiloelectronvolt gas phase collisions may be required to achieve similar ion fragmentation. Higher internal energy transfer to an ion can be achieved in SID than with gas phase CID processes allowing the possibility of fragmenting large, ions, even those with a large number of degrees of freedom and low numbers of charges. Also, the ion collisional energy distributions can be more tightly controlled with SID when compared with gas phase CID processes. A variety of collision surfaces have been used in SID experiments ranging from metal conductive surfaces such as copper and stainless steel to self-assembled aklyl-monolayer surfaces such as octadecanethiolate (CH3(CH2)17SAu), ferrocence terminated self assembled aklyl-monolayer surfaces and fluorinated self-assembled monolayer (F-SAM) surfaces (CF3(CF2)7(CH2)2 SAu). The self-assembled monolayer surfaces tend to reduce the charge loss to the surface during the SID process. Winger et. al. Rev. Sci. Instrum., Vol 63, No. 12, 1992 have reported SID studies using a magnetic sector-dual electric sector-quadrupole (BEEQ) hybrid instrument. They showed kinetic energy distributions of up to +/−3 eV for parent and fragment ions leaving a perdeuterated alkyl-monolayer surface after a 25 eV collision. SID collisions have been performed by impacting ions traversing a Time-OF-Flight flight tube onto surfaces positioned in the flight tube and Time-OF-Flight mass to charge analyzing the resulting ion population. Some degree of mass to charge selection prior to SID fragmentation has been achieved by timing the deflection of ions as the initial pulsed ion packet traverses the flight tube. SID surfaces have been positioned in the field free regions and at the bottom of ion reflector lens assemblies in TOF mass analyzers. The resulting TOF mass spectra of the SID fragment ions in these instruments generally have low resolving power and low mass measurement accuracy due in part to the broad energy distributions of the SID fragment ions leaving the surface. A population of ions acquiring a kinetic energy spread during its flight path or during a re-acceleration step in an ion reflector degrades TOF performance. One embodiment of the present invention reduces the broad kinetic energy distributions of ions produced by SID fragmentation prior to conducting Time-Of-Flight mass analysis. In the present invention, one or more steps of ion mass to charge selection and CID fragmentation can be conducted prior to performing a SID fragmentation step in the TOF pulsing region.
The present invention relates to the configuration and operation of a Time-Of-Flight mass analyzer in a manner that results in improved TOF performance and range of TOF analytical capability. Ions produced from an ion source are directed to a region that contains a pseudo potential energy well located in the pulsing or first acceleration region of a Time-Of-Flight mass analyzer prior to accelerating the ions into the Time-Of-Flight tube drift region. Ions in a wide range of mass-to-charge may be trapped and collected in the pseudo potential well prior to accelerating the collected ions into the Time-Of-Flight drift tube region. Such trapping and collecting of ions that may flow continuously into the TOF pulsing region between acceleration pulses improves the duty cycle efficiency of the TOF, resulting in improved sensitivity. Additional improvements in duty cycle efficiency may be realized when the trapping and collection of ions in a pseudo potential well in the TOF pulsing region is coupled to and coordinated with the trapping and release of ions in an ion guide external to the TOF pulsing region. Also, the resulting constraints on the spatial and energy distributions of the collected ion population prior to pulsing into the TOF drift region improves Time-Of-Flight mass resolving power and mass accuracy. Compression of the spatial and velocity distributions of the ion population by directing the ions to gently collide with a surface or with inert gas in conjunction with ion trapping and collection results in additional improvement to the mass resolving power, mass accuracy, and sensitivity. Ions that are detrimental to the mass analysis, such as MALDI matrix ions of high abundance and low mass that may saturate the detector, may be eliminated by selection of the range of mass-to-charge values that is trapped.
Ions can also be directed to collide with an electrode surface with relatively high impact energy, resulting in surface-induced dissociation. The fragment ions can be collected and accumulated in the pseudo potential well and may optionally be cooled by collisions with the surface or inert gas, prior to accelerating the collected ions into the TOF drift tube for mass analysis. Mass analysis of such fragment ions can improve the mass-to-charge measurement accuracy and quantification performance. Performing SID directly in the TOF acceleration region avoids the loss of fragment ions that inevitably occurs when SID is performed external to the TOF acceleration region followed by transport of the fragment ions into the TOF acceleration region prior to TOF mass analysis. Hence, the present invention improves sensitivity for MS/MS analysis using SID or CID.
In one embodiment of the invention, ions entering the TOF first accelerating region are directed toward the bottom of the pseudo potential well by applying a reverse electric field in the TOF acceleration region. Ions collected in the pseudo potential well are accelerated into the flight tube of a Time-Of-Flight mass analyzer by applying a forward electric field in the TOF acceleration region. The collection of ions in the pseudo potential well and forward acceleration of ion packets can occur at repetition rates exceeding 20 kilohertz allowing TOF pulse repetition rates typically used in atmospheric pressure ion source orthogonal pulsing TOF ion mass-to-charge analysis.
A variety of ion sources can be configured according to the invention with the ability to conduct SID with TOF mass analysis. Ions can be produced directly in the TOF first acceleration region or produced external to the first acceleration region. A time-of-flight mass spectrometer configured according to the invention can be selectively operated with or without collection of ions in a pseudo potential well, surface induced dissociation, reaction of ions with surfaces, or collisional cooling by introduction of a collisional cooling gas or controlled collisions with a surface, prior to Time-Of-Flight mass analysis. The invention retains the ability to conduct existing ionization and TOF analysis techniques. The added ion collection, trapping, and collisional cooling in a pseudo potential well and SID fragmentation capabilities expands the overall analytical range of a Time-Of-Flight mass analyzer. A Time-Of-Flight mass analyzer configured and operated according to the invention can be incorporated into a hybrid instrument enhancing MS/MS or MS/MSn operation. Such an instrument may be configured with a range of atmospheric pressure or vacuum ion sources.